Should the reflection map somehow be coupled with the water mesh surface?
I think so... but you are being terribly unspecific about 'reflection map.' So you're rendering from a mirrored camera? Well then yeah, if you have this 'coupling' configured to support any sort of reflection mapping technique, then I guess that would be quite good. It's very standard and sensible to have your reflection map seperate from the material. Reflection maps are applied/shared by meshs in the context of the environment (though sometimes blurred etc) and a material is merely... a material.
do I just perform a simple query to find out which render items require a reflection map to be generated by the engine?
You seem to be fishing pretty far out. I think you'll know what to do when you get to it. Otherwise, this is kind of a vague question.